BOSC 2012 Call for Abstracts
by Brad Chapman
Call for Abstracts for the 13th Annual Bioinformatics Open Source Conference (BOSC 2012)
A Special Interest Group (SIG) of ISMB 2012
Dates: July 13-14, 2012
Location: Long Beach, California
Web site: http://www.open-bio.org/wiki/BOSC_2012
Email: bosc(a)open-bio.org
BOSC announcements mailing list: http://lists.open-bio.org/mailman/listinfo/bosc-announce
Important Dates:
April 13, 2012: Deadline for submitting abstracts
May 7, 2012: Notification of accepted talk abstracts emailed to authors
July 11-12, 2012: Codefest 2012 programming session
July 13-14, 2012: BOSC 2012
July 15-17, 2012: ISMB 2012
The Bioinformatics Open Source Conference (BOSC) is sponsored by the
Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated
to promoting the practice and philosophy of Open Source software
development within the biological research community. To be considered
for acceptance, software systems representing the central topic in a
presentation submitted to BOSC must be licensed with a recognized Open
Source License, and be freely available for download in source code
form.
We invite you to submit one-page abstracts for talks and posters. This year's session topics are:
- Cloud and Parallel Computing
- Linked Data
- Genome-scale Data Management
- Data Visualization and Imaging
- Translational Bioinformatics
- Software Interoperability (possibly a joint session with BSI-SIG,
the Bioinformatics Software Interoperability SIG)
- Bioinformatics Open Source Project Updates
- Interfacing with Industry (panel)
Thanks to generous sponsorship from Eagle Genomics and an anonymous
donor, we are pleased to announce a competition for three Student
Travel Awards. Each winner will be awarded $250 to defray the costs of
travel to BOSC 2012.
For instructions on submitting your abstract, please visit
http://www.open-bio.org/wiki/BOSC_2012#Submitting_Abstracts
BOSC 2012 Organizing Committee:
Nomi Harris (chair), Jan Aerts, Brad Chapman, Peter Cock, Chris Fields, Erwin Frise, Peter Rice
10 years, 4 months
Defining Job Runners Dynamically
by John Chilton
Hello All,
I just issued a pull request that augments Galaxy to allow defining
job runners dynamically at runtime
(https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-r...).
Whether it makes the cut or not, I thought I would describe enhancements
here in case anyone else would find it useful.
There a couple use cases we hope this will help us address for our
institution - one is dynamically switching queues based on user (we have
a very nice shared memory resource that can only be used by researchers
with NIH funding) and the other is inspecting input sizes to give more
accurate max walltimes to pbs (a small number of cufflinks jobs for
instance take over three days on our cluster but defining max walltimes
in excess of that for all jobs could result in our queue sitting idle
around our monthly downtimes). You might also imagine using this to
dynamically switch queues entirely based on input sizes or parameters,
or alter queue priorities based on the submitting user or input
sizes/parameters.
There are two steps to use this - you must add a line in universe.ini
and define a function to compute the true job runner string in the new
file lib/galaxy/jobs/rules.py.
This first step is similar to what you would do to statically assign
a tool to a particular job runner. If you would like to dynamically
assign a job runner for cufflinks you would start by adding a line like
one of the following to universe.ini
cufflinks = dynamic:///python
-or-
cufflinks = dynamic:///python/compute_runner
If you use the first form, a function called cufflinks must be defined
in rules.py, adding the extra argument after python/ lets you specify a
particular function by name (compute_runner in this example). This
second option could let you assign job runners with the same function
for multiple tools.
The only other step is to define a python function in rules.py that
produces a string corresponding to a valid job runner such as
"local:///" or "pbs:///queue/-l walltime=48:00:00/".
If the functions defined in this file take in arguments, these arguments
should have names from the follow list: job_wrapper, user_email, app,
job, tool, tool_id, job_id, user. The plumbing will map these arguments
to the implied galaxy object. For instance, job_wrapper is the
JobWrapper instance for the job that gets passed to the job runner,
user_email is the user's email address or None, app is the main
application configuration object used throughout the code base that can
be used for instance to get values defined in universe.ini, job, tool,
and user are model objects, and job_id and tool_id the relevant ids.
If you are writing a function that routes a certain list of users to a
particular queue or increases their priority, you will probably only
need to take in one argument - user_email. However, if you are going to
look at input file sizes you may want to take in an argument called job
and use the following piece of code to find the input size for input
named "input1" in the tool xml.
inp_data = dict( [ ( da.name, da.dataset ) for da in
job.input_datasets ] )
inp_data.update( [ ( da.name, da.dataset ) for da in
job.input_library_datasets ] )
input1_file = inp_data[ "input1" ].file_name
input1_size = os.path.getsize( input1_file )
This whole concept works for a couple of small tests on my local
machine, but there are certain aspects of the job runner code that makes
me feel there may be corner cases I am not seeing where this approach
may not work - so your millage may vary.
-John
------------------------------------------------
John Chilton
Software Developer
University of Minnesota Supercomputing Institute
Office: 612-625-0917
Cell: 612-226-9223
E-Mail: chilton(a)msi.umn.edu
10 years, 4 months
Production environment and Apache's sendfile
by Jennifer Jackson
Hello,
I am going to forward you question to the galaxy-dev(a)bx.psu.edu mailing
list so that the development community can offer advice.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists
Thanks,
Jen
Galaxy team
On 3/2/12 8:00 AM, Yuri D'Elia wrote:
> Hi everyone. I've set up a galaxy production environment and it seems to be working.
> I've identified a couple of issues though:
>
> If I enable apache_xsendfile, the little "eye" icon ("Display data in browser") on each dataset stops working. I get the following instead:
>
> The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this server
>
> My document root is not the same as the galaxy root (as suggested). Everything else seems to work. Is this a bug?
>
> Second question:
>
> I want to rotate the galaxy log file (as specified with paster.py serve --log-file. I can't find a way to reopen the logfile in galaxy without taking down the whole service, or a way to redirect the log to a pipe together while using --daemon.
>
> I cannot let the file grow forever.
> Any suggestions?
>
> Thanks.
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
10 years, 4 months
snpEff: html report is not displaying after update
by Jennifer Jackson
Hello Raj,
This tool is from the Tool Shed and is maintained by the tool author. To
contact them about functionality or problems, go to the Tool Shed at
http://toolshed.g2.bx.psu.edu/, locate the repository (search by
'snpEff'), click on the name, in the the top far right corner locate the
pull down menu "Repository Actions". Select "Contact repository owner"
to send them a message.
There have been many updates to Galaxy recently and it is possible that
one of these had an impact on this tool. I am going to send your email
to galaxy-dev(a)bx.psu.edu, to see if anyone else has had problems with
this tool since the last distribution update.
You may be asked to provide more information (be as specific as you
can): the hg pull #, any customizations, python version, etc.
Regards,
Jen
Galaxy team
On 2/14/12 8:28 PM, Praveen Raj Somarajan wrote:
> Hi All,
>
> I updated galaxy recently to the latest version. Everything looks fine,
> except snpEff report html view. It was displaying properly (all tables
> and summary values) before the update, but the summary values are not
> displaying after the update. A sample screen-shot is attached for your
> reference. Could you please figure out this issue?
>
> When I ran the same on command line, the reports were generated
> correctly. I assume, something (datatypes or preview) has changed by the
> update. Please let me know the work around on this?
>
> Secondly, as we know, snpEff also generates a gene-wise annotation file
> along with other results, but somehow we cannot access this file through
> Galaxy. Though we see the link in the html report, but it seems the path
> is broken.
>
> Let me know your suggestions.
>
> Best,
>
> Raj
>
>
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> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
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>
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>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
10 years, 4 months
Problems getting galaxy to start
by michael burrell (NBI)
Good evening,
I am having difficulty getting galaxy to startup over the last couple of days, I initially suspected that it was an issue with the eggs, but have replaced these and the following errors remain,
galaxy@jic55119: $ python --version
Python 2.6.6
galaxy@jic55119:galaxy-central$ ./run.sh
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in <module>
command.run()
File "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run
invoke(command, command_name, options, args[1:])
File "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke
exit_code = runner.run(args)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run
result = self.command()
File "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command
relative_to=base, global_conf=vars)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp
**kw)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj
global_conf=global_conf)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext
global_conf=global_conf)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 413, in get_context
section)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit
value = import_string(found_expr)
File "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/home/home/galaxy/software/galaxy-central/lib/pkg_resources.py", line 1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/home/home/galaxy/software/galaxy-central/lib/galaxy/web/buildapp.py", line 19, in <module>
from galaxy import config, jobs, util, tools
File "/home/home/galaxy/software/galaxy-central/lib/galaxy/jobs/__init__.py", line 4, in <module>
from galaxy import util, model
EOFError: EOF read where object expected
Any suggestions?
Thanks in advance
Michael.
10 years, 4 months
large ftp uploads to galaxy cloud
by bermans＠mskcc.org
I'm having difficulty uploading files > 6GB or so to an EC2 instantiation of galaxy cloud. The size seems to correlate with the amount of space available on the root volume. I can upload a 5.06 GB file but any larger and it never shows up in the galaxy upload history. I'm using a "Large" EC2 instance but the root volume is only 15GB and only has 5.9GB free.
I'm using the 861460482541/galaxy-cloudman-2011-03-22
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10 years, 4 months
functional test issue - PDF output file comparison
by Anne Pajon
Dear All,
I have noticed that some output files of functional tests are of type PDF. When comparing the one produced by the tool and the one stored in test-data/, they obviously differ even if they visually look identical.
Is there a better way to compare PDF files within Galaxy than using diff? If not, do you have experience or suggestion at solving these functional test failures?
Thanks a lot in advance.
Kind regards,
Anne.
--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
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10 years, 4 months
Problem with python ./scripts/make_egg_packager.py
by Jose William Valero Velasquez
Hi,
I'm writing you because i'm trying to install galaxy in a server running
suse behind a proxy, so i have to build the eggs like if the server were
offline, in the guide says that i should execute the
command ./scripts/make_egg_packager.py but i get the following error, and i
don't really understand whats happening:
File "scripts/make_egg_packager.py", line 21, in <module>
c = Crate()
TypeError: __init__() takes at least 2 arguments (1 given)
I'd really apreciate your help to figure out how to solve this issue.
William Valero
Universidad Nacional de Colombia.
10 years, 4 months
Progress indicators/feedback for long jobs on Galaxy
by Jennifer Jackson
Hi Greg,
I am going to forward your email over to the galaxy-dev(a)bx.psu.edu
mailing list where the development community can provide feedback.
Best,
Jen
Galaxy team
On 3/4/12 3:26 PM, Greg Edwards wrote:
> Hi,
>
> This has been raised a number of times .. one issue is at ...
>
> https://bitbucket.org/galaxy/galaxy-central/issue/250/progress-of-running...
>
> but seems to have been dropped from Open to On Hold. There was another
> similar request in the issues list but I can't find it just now.
>
> I'd be gald to know if anything is happening on the idea of simple
> progress indicators. The first things that were raised by my "users"
> were 1) Don't know how long a data upload is going to take, and b) Don't
> know what's happening with my tool execution. (And these were both
> operations of only 5-10 minutes or so, they'd go crazy with the multi-GB
> uploads and hours-long runs I see reported here).
>
>
> I've implemented my own email-based scheme on a AWS EC2 CloudMan Galay,
> seems to be working ok. It uses an Ubuntu package "sendEmail", which is
> a self-conatined simple SMTP email sender. It sends progress emails out
> of the main Perl tool code, via a bash script, every 1 to N minutes
> (selectable), to an email address supplied by the user. The emails have
> configurable subject and content with brief display of Start, Progress
> (every N minutes) and Success/Failure termination status.
>
> You have to jump through some hurdles. AWS thinks your'e a spammer and
> blocks emails after a while ! but you can submit a request to get around
> that.
>
> If anyone's interested let me know.
>
> Cheers,
> Greg E
>
>
> --
> Greg Edwards,
> Port Jackson Bioinformatics
> gedwards2(a)gmail.com <mailto:gedwards2@gmail.com>
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
10 years, 4 months
Dynamic feedback whilst setting tool-parameters in Galaxy web-interface
by Tim Dorscheidt
Hi,
I've been writing several wrapper-files for statistical tools, and I was wondering whether it was possible to enhance the tool-interface currently available in the Galaxy web-interface. Ideally, I am looking for options to already display (some) tool-feedback in the user-interface of a tool dependent on the dataset selected from the "history" and user-defined parameters. An example would be a graph re-drawing itself every time the user selects a different dataset or alters a parameter, but simple text-feedback that dynamically updates itself would be a great start already. The "execute" button is now the only way to run code on user-input, and this makes Galaxy a rather cumbersome environment in the case of tools that require many iterations (or just when playing around with parameters).
So far, the only limited example I've seen of such "dynamic feedback" is when the user select a matrix from her "history" and Galaxy is able to read the amount of columns, which strictly speaking is a form of generating immediate feedback on the basis of user-selected input, but of course I'd like to define the code myself that is run on the input and what sort of feedback is derived and displayed from this.
I have seen the new "visualizations" section of Galaxy, which indeed allows for some of this, but it is clearly separate from the standard tool-funcitonality of Galaxy, and it does not allow for workflows (whereas the above functionality does not clash with workflows, which simply needs to access the static version of the tool).
Any help would be greatly appreciated.
Tim Dorscheidt
Scientific Programmer
Biosystems Data Analysis group, SILS
University of Amsterdam
10 years, 4 months
